AutoCloner

Multiple sequence alignment - TraesCS2A01G339700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS2A01G339700	chr2A	100.000	2543	0	0	1	2543	574266703	574264161	0.000000e+00	4697
1	TraesCS2A01G339700	chr2A	89.730	2590	213	27	1	2543	518129034	518131617	0.000000e+00	3260
2	TraesCS2A01G339700	chr2A	89.043	2592	214	32	1	2543	460466566	460469136	0.000000e+00	3149
3	TraesCS2A01G339700	chr2A	90.094	2352	206	13	1	2327	657758176	657755827	0.000000e+00	3027
4	TraesCS2A01G339700	chr3A	90.835	2564	205	15	1	2543	114183451	114186005	0.000000e+00	3406
5	TraesCS2A01G339700	chr3A	90.730	1877	173	1	4	1880	407690971	407689096	0.000000e+00	2501
6	TraesCS2A01G339700	chr6A	88.940	2586	217	33	1	2543	601316009	601318568	0.000000e+00	3127
7	TraesCS2A01G339700	chr6A	91.288	1033	73	10	1512	2543	365171021	365170005	0.000000e+00	1393
8	TraesCS2A01G339700	chr6A	90.244	410	26	4	2134	2543	171927880	171928275	8.060000e-145	523
9	TraesCS2A01G339700	chr2D	91.849	1877	152	1	4	1880	297119382	297117507	0.000000e+00	2617
10	TraesCS2A01G339700	chr3D	91.170	1880	166	0	4	1883	272659429	272657550	0.000000e+00	2553
11	TraesCS2A01G339700	chr3D	90.866	1883	148	9	1	1879	150778257	150780119	0.000000e+00	2503
12	TraesCS2A01G339700	chr1A	90.241	1947	181	4	603	2543	130526254	130528197	0.000000e+00	2534
13	TraesCS2A01G339700	chr1A	89.196	1953	177	15	603	2543	130586293	130588223	0.000000e+00	2407
14	TraesCS2A01G339700	chr4A	89.134	1408	104	9	1158	2543	507416196	507414816	0.000000e+00	1707

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS2A01G339700	chr2A	574264161	574266703	2542	True	4697	4697	100.000	1	2543	1	chr2A.!!$R1	2542
1	TraesCS2A01G339700	chr2A	518129034	518131617	2583	False	3260	3260	89.730	1	2543	1	chr2A.!!$F2	2542
2	TraesCS2A01G339700	chr2A	460466566	460469136	2570	False	3149	3149	89.043	1	2543	1	chr2A.!!$F1	2542
3	TraesCS2A01G339700	chr2A	657755827	657758176	2349	True	3027	3027	90.094	1	2327	1	chr2A.!!$R2	2326
4	TraesCS2A01G339700	chr3A	114183451	114186005	2554	False	3406	3406	90.835	1	2543	1	chr3A.!!$F1	2542
5	TraesCS2A01G339700	chr3A	407689096	407690971	1875	True	2501	2501	90.730	4	1880	1	chr3A.!!$R1	1876
6	TraesCS2A01G339700	chr6A	601316009	601318568	2559	False	3127	3127	88.940	1	2543	1	chr6A.!!$F2	2542
7	TraesCS2A01G339700	chr6A	365170005	365171021	1016	True	1393	1393	91.288	1512	2543	1	chr6A.!!$R1	1031
8	TraesCS2A01G339700	chr2D	297117507	297119382	1875	True	2617	2617	91.849	4	1880	1	chr2D.!!$R1	1876
9	TraesCS2A01G339700	chr3D	272657550	272659429	1879	True	2553	2553	91.170	4	1883	1	chr3D.!!$R1	1879
10	TraesCS2A01G339700	chr3D	150778257	150780119	1862	False	2503	2503	90.866	1	1879	1	chr3D.!!$F1	1878
11	TraesCS2A01G339700	chr1A	130526254	130528197	1943	False	2534	2534	90.241	603	2543	1	chr1A.!!$F1	1940
12	TraesCS2A01G339700	chr1A	130586293	130588223	1930	False	2407	2407	89.196	603	2543	1	chr1A.!!$F2	1940
13	TraesCS2A01G339700	chr4A	507414816	507416196	1380	True	1707	1707	89.134	1158	2543	1	chr4A.!!$R1	1385

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
283	346	0.322098	CCGGATTGTGGTGGCAACTA	60.322	55.0	3.27	0.0	37.61	2.24	F
481	544	0.322546	TCGCTGTCTGTCTAGCCTCA	60.323	55.0	0.00	0.0	36.60	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1090	1158	0.458543	CACCAGCTAGTCGCGAACAT	60.459	55.0	12.06	2.05	45.59	2.71	R
2201	2286	0.679321	TGCAACGCATGGGCATCTTA	60.679	50.0	10.10	0.00	41.24	2.10	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
86	87	1.287815	CACGCACCCGTCTTCTGTA	59.712	57.895	0.00	0.00	46.39	2.74
92	93	1.204704	CACCCGTCTTCTGTATCTGCA	59.795	52.381	0.00	0.00	0.00	4.41
184	227	4.771356	GCAGTACGACGCGGCAGA	62.771	66.667	14.85	0.00	0.00	4.26
263	326	2.243957	CGAGTTGCTGAACCACGCA	61.244	57.895	0.00	0.00	31.81	5.24
272	335	1.964373	GAACCACGCACCGGATTGT	60.964	57.895	9.46	0.00	0.00	2.71
283	346	0.322098	CCGGATTGTGGTGGCAACTA	60.322	55.000	3.27	0.00	37.61	2.24
316	379	2.232941	CCAAGCAAGGTTGATGAAGCAT	59.767	45.455	13.10	0.00	31.56	3.79
390	453	2.355193	GCCAGAGAACGGCTCCTCT	61.355	63.158	4.21	0.00	46.56	3.69
462	525	1.078143	GAGGGGTGCGATTCTTGCT	60.078	57.895	0.00	0.00	0.00	3.91
475	538	1.534729	TCTTGCTCGCTGTCTGTCTA	58.465	50.000	0.00	0.00	0.00	2.59
481	544	0.322546	TCGCTGTCTGTCTAGCCTCA	60.323	55.000	0.00	0.00	36.60	3.86
484	547	2.359214	CGCTGTCTGTCTAGCCTCATTA	59.641	50.000	0.00	0.00	36.60	1.90
500	563	4.444306	CCTCATTAAAATAGAGGGCGGACA	60.444	45.833	0.00	0.00	44.10	4.02
503	566	2.403252	AAAATAGAGGGCGGACAGTG	57.597	50.000	0.00	0.00	0.00	3.66
514	577	2.431683	GACAGTGGGAGCTTGGCA	59.568	61.111	0.00	0.00	0.00	4.92
559	622	2.519541	CGGATGGGAGGAGCTCGA	60.520	66.667	7.83	0.00	0.00	4.04
650	713	1.817357	CGGGTTTAACAGAGGGGTTC	58.183	55.000	0.00	0.00	32.29	3.62
682	745	2.904866	GGCGTGTTCAGTTGGGCA	60.905	61.111	0.00	0.00	0.00	5.36
717	780	5.411361	AGCGCAGTACTATTTGATTTGACAA	59.589	36.000	11.47	0.00	0.00	3.18
755	818	3.867857	TGATACGGCTTTAATGCAGACA	58.132	40.909	17.96	12.09	34.04	3.41
769	833	0.909610	CAGACAAGGGAGGGGTAGCA	60.910	60.000	0.00	0.00	0.00	3.49
775	839	1.307084	GGGAGGGGTAGCAGTTCCT	60.307	63.158	8.04	0.00	0.00	3.36
782	846	2.026262	GGGGTAGCAGTTCCTGAAATGA	60.026	50.000	11.16	0.00	38.53	2.57
788	852	4.401022	AGCAGTTCCTGAAATGATGAACA	58.599	39.130	11.16	0.00	38.53	3.18
849	913	2.478292	TGAGGGAAGTAATGGGAGGAC	58.522	52.381	0.00	0.00	0.00	3.85
865	929	1.538687	GGACGACCGGGAAAAGAGGA	61.539	60.000	6.32	0.00	0.00	3.71
946	1010	1.456296	TCTACCACATCGTACGCACT	58.544	50.000	11.24	0.00	0.00	4.40
978	1042	2.165845	CCTAAGCACCTACACTAAGCGT	59.834	50.000	0.00	0.00	0.00	5.07
1102	1170	0.098200	CCAGACGATGTTCGCGACTA	59.902	55.000	9.15	0.00	45.12	2.59
1143	1211	0.956633	ACGCCAACTACGACTCTCAA	59.043	50.000	0.00	0.00	0.00	3.02
1201	1269	0.539051	CATCCTCAAGAAGCTCGGGT	59.461	55.000	0.00	0.00	0.00	5.28
1224	1292	1.741706	GACATCGTCGTACTCCTCCAA	59.258	52.381	0.00	0.00	0.00	3.53
1263	1331	1.006998	TCATTGCCTGCCACCCTAATT	59.993	47.619	0.00	0.00	0.00	1.40
1332	1400	3.774702	GCCGACGCCACGAAGAAC	61.775	66.667	0.00	0.00	35.09	3.01
1422	1490	5.237127	CCACATGTACGAGCAAATCATGTAT	59.763	40.000	0.00	0.00	44.38	2.29
1534	1603	1.961277	CTCGCCACAAAAGTCGCCT	60.961	57.895	0.00	0.00	0.00	5.52
1543	1612	2.633481	ACAAAAGTCGCCTCTCCTTAGT	59.367	45.455	0.00	0.00	0.00	2.24
1826	1899	4.261801	GGGCATCTTGCTAGAAACACTAA	58.738	43.478	0.99	0.00	44.28	2.24
1844	1917	2.102070	AAAACATGTCGGACCGCATA	57.898	45.000	18.99	5.46	0.00	3.14
1935	2008	5.047092	CCAGTAAAAGGAAAAGGCATGTCAT	60.047	40.000	0.00	0.00	0.00	3.06
2020	2094	1.272807	TAGCTAGGGAAGGCGTGTTT	58.727	50.000	0.00	0.00	0.00	2.83
2082	2161	1.402720	CCAACTATTGGCAAACCGCAG	60.403	52.381	3.01	0.00	45.17	5.18
2260	2347	9.008965	TGCATTTGTATGAGTAGTTTATGTTGT	57.991	29.630	0.00	0.00	33.37	3.32
2318	2405	3.330720	GTGGAGAGGGGTGTGGGG	61.331	72.222	0.00	0.00	0.00	4.96
2319	2406	3.869934	TGGAGAGGGGTGTGGGGT	61.870	66.667	0.00	0.00	0.00	4.95
2320	2407	2.531942	GGAGAGGGGTGTGGGGTT	60.532	66.667	0.00	0.00	0.00	4.11
2327	2414	1.045407	GGGGTGTGGGGTTTCTTTTC	58.955	55.000	0.00	0.00	0.00	2.29
2388	2475	3.719268	ATCGGATGGCCTATATTGCAA	57.281	42.857	3.32	0.00	0.00	4.08
2398	2485	3.759581	CCTATATTGCAAGATGGCAGGT	58.240	45.455	16.68	0.00	45.88	4.00
2418	2505	2.496899	ACACCATCATCACCAACTCC	57.503	50.000	0.00	0.00	0.00	3.85
2527	2658	7.259088	ACTAGTTGGTTACCAAATCTCATCT	57.741	36.000	20.58	12.54	45.73	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
86	87	1.435925	CAACGCCATGCATGCAGAT	59.564	52.632	26.69	7.33	0.00	2.90
169	212	2.745100	TCTCTGCCGCGTCGTACT	60.745	61.111	4.92	0.00	0.00	2.73
263	326	1.901464	GTTGCCACCACAATCCGGT	60.901	57.895	0.00	0.00	37.16	5.28
272	335	2.167398	GACGGAGCTAGTTGCCACCA	62.167	60.000	9.93	0.00	44.23	4.17
390	453	0.323629	CCACTCTTCCGGTGGCTTTA	59.676	55.000	0.00	0.00	45.97	1.85
398	461	2.290323	ACCATTTTCTCCACTCTTCCGG	60.290	50.000	0.00	0.00	0.00	5.14
462	525	0.322546	TGAGGCTAGACAGACAGCGA	60.323	55.000	0.00	0.00	38.73	4.93
475	538	3.496870	CCGCCCTCTATTTTAATGAGGCT	60.497	47.826	0.00	0.00	44.32	4.58
481	544	4.451900	CACTGTCCGCCCTCTATTTTAAT	58.548	43.478	0.00	0.00	0.00	1.40
484	547	1.065418	CCACTGTCCGCCCTCTATTTT	60.065	52.381	0.00	0.00	0.00	1.82
500	563	4.357279	GCCTGCCAAGCTCCCACT	62.357	66.667	0.00	0.00	0.00	4.00
559	622	1.267533	GGAATTAAACGCAACACCGGT	59.732	47.619	0.00	0.00	0.00	5.28
650	713	4.292178	GCCTCCTCGCCTCCATCG	62.292	72.222	0.00	0.00	0.00	3.84
693	756	4.935205	TGTCAAATCAAATAGTACTGCGCT	59.065	37.500	9.73	0.00	0.00	5.92
755	818	0.914902	GGAACTGCTACCCCTCCCTT	60.915	60.000	0.00	0.00	0.00	3.95
769	833	3.760684	GGCTGTTCATCATTTCAGGAACT	59.239	43.478	0.00	0.00	40.12	3.01
775	839	5.656480	CATCATTGGCTGTTCATCATTTCA	58.344	37.500	0.00	0.00	0.00	2.69
782	846	2.364324	GGATGCATCATTGGCTGTTCAT	59.636	45.455	27.25	0.00	0.00	2.57
788	852	0.851469	AGGAGGATGCATCATTGGCT	59.149	50.000	27.25	14.85	0.00	4.75
849	913	1.090052	GCATCCTCTTTTCCCGGTCG	61.090	60.000	0.00	0.00	0.00	4.79
865	929	1.466192	CGTTGCATTCACATCGTGCAT	60.466	47.619	0.00	0.00	46.90	3.96
978	1042	2.038557	GGGTCTGGAGTGAGCACTTTTA	59.961	50.000	4.42	0.00	42.66	1.52
1090	1158	0.458543	CACCAGCTAGTCGCGAACAT	60.459	55.000	12.06	2.05	45.59	2.71
1143	1211	2.292267	GCAACGATCATCTGGTCCAAT	58.708	47.619	0.00	0.00	0.00	3.16
1201	1269	3.136763	GGAGGAGTACGACGATGTCATA	58.863	50.000	0.00	0.00	32.09	2.15
1277	1345	2.173569	ACCAGTGCTTGAAAGAGGTTCT	59.826	45.455	0.00	0.00	37.13	3.01
1422	1490	6.440647	CCTCAATGGCCTTGTAGATACCTATA	59.559	42.308	3.32	0.00	36.20	1.31
1534	1603	2.110967	CGACCGGCGACTAAGGAGA	61.111	63.158	9.30	0.00	44.57	3.71
1565	1634	1.760029	CCTCCTCCTCCTCAACTTAGC	59.240	57.143	0.00	0.00	0.00	3.09
1826	1899	1.939934	CATATGCGGTCCGACATGTTT	59.060	47.619	23.16	10.86	0.00	2.83
1844	1917	1.358725	CGCATCGTCGGTTTGGTCAT	61.359	55.000	0.00	0.00	0.00	3.06
2020	2094	5.183713	CCACATGAAAGTGAAAATGCTAGGA	59.816	40.000	0.00	0.00	42.05	2.94
2103	2182	4.530946	AGATCTTCCCCTCGTTTCTGTTTA	59.469	41.667	0.00	0.00	0.00	2.01
2201	2286	0.679321	TGCAACGCATGGGCATCTTA	60.679	50.000	10.10	0.00	41.24	2.10
2259	2346	4.398319	TCTTGTTCATCCTTTTCTCCCAC	58.602	43.478	0.00	0.00	0.00	4.61
2260	2347	4.350816	TCTCTTGTTCATCCTTTTCTCCCA	59.649	41.667	0.00	0.00	0.00	4.37
2374	2461	2.158490	TGCCATCTTGCAATATAGGCCA	60.158	45.455	23.02	14.58	38.56	5.36
2398	2485	2.093711	CGGAGTTGGTGATGATGGTGTA	60.094	50.000	0.00	0.00	0.00	2.90
2468	2599	3.350219	TTGCACCCAAATCTCTACTCC	57.650	47.619	0.00	0.00	0.00	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.